I'm able to reproduce this non-deterministic behavior with a straightforward modification of BoxExample wherein a texture in added to the root after rendering has begun.

main() {
start(BoxExample.class)

// add a texture to root here
}

Instead of Box I use Quads at different depths and turn-off the depth test. I think it's fair to say the problem is related to modify the scene after drawing has begun. Seems okay with now texture, just colored verts, so maybe issue with RenderStates and traversal of the graph?